Contacts of the helix formed by residues 38 - 49 (chain M) in PDB entry 6AH0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 38 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30I A 3.4 24.8 + - - -
32I G 3.3 6.1 - - - -
36M ARG 4.1 0.4 + - - -
37M LYS* 1.3 73.7 - - - +
39M ALA* 1.3 67.8 + - - -
40M ASN 3.2 3.7 + - - -
41M GLU 3.2 2.0 + - - -
42M ALA* 2.9 21.1 + - - -
99M VAL* 6.1 0.2 - - - +
101M ALA 2.9 21.3 + - - +
102M CYS* 4.9 0.2 - - - -
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Residues in contact with ALA 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I A 4.8 2.4 + - - -
31I U 4.9 7.4 + - - -
32I G 3.4 4.0 + - - -
245L PRO* 6.1 1.3 - - - -
38M GLY* 1.3 71.0 - - - +
40M ASN* 1.3 56.5 + - - +
42M ALA* 3.1 1.7 + - - +
43M THR* 2.9 27.7 + - - -
65M ILE 5.9 2.9 - - - -
66M ILE* 6.4 1.6 - - - +
101M ALA* 4.1 15.8 + - - +
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Residues in contact with ASN 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I G 2.8 22.9 + - - -
43I G 5.3 6.3 - - - -
245L PRO* 5.2 14.1 - - - +
246L ALA 5.8 1.3 - - - +
39M ALA* 1.3 69.2 - - - +
41M GLU* 1.3 61.3 + - - +
43M THR* 3.2 3.9 + - - +
44M LYS* 3.1 17.5 + - - -
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Residues in contact with GLU 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I G 3.8 7.5 + - - +
43I G 5.6 7.6 + - - -
36M ARG* 5.5 8.7 - - - +
37M LYS 5.2 6.9 + - - +
38M GLY* 3.2 5.5 + - - -
40M ASN* 1.3 72.4 - - - +
42M ALA* 1.3 63.8 + - - +
44M LYS* 3.4 3.1 + - - +
45M THR* 3.2 18.0 + - - -
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Residues in contact with ALA 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36M ARG 5.2 2.1 + - - -
38M GLY 2.9 15.1 + - - -
39M ALA* 3.6 4.0 - - - +
41M GLU* 1.3 73.4 - - - +
43M THR* 1.3 67.7 + - - +
45M THR* 3.3 3.3 + - - +
46M LEU* 3.3 15.2 + - - -
102M CYS* 5.2 3.4 - - - +
103M SER* 5.0 18.4 - - - +
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Residues in contact with THR 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39M ALA 2.9 14.3 + - - -
40M ASN* 3.2 4.2 + - - +
42M ALA* 1.3 76.2 - - - +
44M LYS* 1.3 62.0 + - - +
46M LEU* 3.0 12.7 + - - +
47M ASN* 3.0 11.3 + - - -
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Residues in contact with LYS 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I C 6.0 2.0 - - - -
40M ASN 3.1 13.1 + - - -
41M GLU* 3.4 4.2 + - - +
42M ALA 3.3 0.4 - - - -
43M THR* 1.3 74.5 - - - +
45M THR* 1.3 57.3 + - - +
46M LEU 3.0 0.3 + - - -
47M ASN* 3.1 3.0 + - - +
48M ARG* 2.8 28.6 + - - -
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Residues in contact with THR 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M GLU 3.2 13.5 + - - -
42M ALA* 3.3 4.6 + - - +
44M LYS* 1.3 74.4 - - - +
46M LEU* 1.3 56.0 + - - +
48M ARG* 5.0 1.1 - - - +
49M GLY* 3.0 5.4 + - - -
50M ILE* 2.9 35.6 + - - +
51M SER* 3.7 9.2 + - - +
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Residues in contact with LEU 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M ALA 3.3 8.4 + - - -
43M THR 3.0 7.7 + - - -
45M THR* 1.3 75.6 - - - +
47M ASN* 1.3 64.8 + - - +
49M GLY* 3.1 13.4 + - - -
51M SER* 5.5 2.2 - - - +
72M LEU 6.5 1.3 - - - -
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Residues in contact with ASN 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43M THR 3.0 13.1 + - - -
44M LYS* 3.7 2.5 - - - +
46M LEU* 1.3 75.9 - - - +
48M ARG* 1.3 60.8 + - - +
49M GLY 3.6 0.2 + - - -
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Residues in contact with ARG 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44M LYS 2.8 16.1 + - - -
45M THR* 4.1 1.3 - - - +
47M ASN* 1.3 76.3 - - - +
49M GLY* 1.3 61.8 + - - +
50M ILE* 3.6 1.8 - - - -
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Residues in contact with GLY 49 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M THR 3.0 6.2 + - - -
46M LEU* 3.1 11.1 + - - -
47M ASN 3.3 0.6 - - - -
48M ARG* 1.3 80.1 - - - +
50M ILE* 1.3 58.0 + - - +
51M SER 3.6 3.3 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il